PGx: Putting Peptides to BED

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2015 Dec 8

PMID 26638927

Citations 9

Authors

Manor Askenazi

Kelly V Ruggles

David Fenyo

Affiliations

Soon will be listed here.

Abstract

Every molecular player in the cast of biology's central dogma is being sequenced and quantified with increasing ease and coverage. To bring the resulting genomic, transcriptomic, and proteomic data sets into coherence, tools must be developed that do not constrain data acquisition and analytics in any way but rather provide simple links across previously acquired data sets with minimal preprocessing and hassle. Here we present such a tool: PGx, which supports proteogenomic integration of mass spectrometry proteomics data with next-generation sequencing by mapping identified peptides onto their putative genomic coordinates.

Citing Articles

Comprehensive Peptide Mapping Is Crucial for Proteogenomics and Proteomics.

Allmer J Methods Mol Biol. 2024; 2859:39-51.

PMID: 39436595 DOI: 10.1007/978-1-0716-4152-1_3.

Variant biomarker discovery using mass spectrometry-based proteogenomics.

Reilly L, Seddighi S, Singleton A, Cookson M, Ward M, Qi Y Front Aging. 2023; 4:1191993.

PMID: 37168844 PMC: 10165118. DOI: 10.3389/fragi.2023.1191993.

Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.

Chen W, Liu X J Proteome Res. 2020; 20(1):261-269.

PMID: 33183009 PMC: 7775893. DOI: 10.1021/acs.jproteome.0c00369.

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner C, Pirklbauer G, Bender A, Steen J, Choudhary J J Vis Exp. 2018; (135).

PMID: 29889196 PMC: 6101353. DOI: 10.3791/57633.

Large Scale Identification of Variant Proteins in Glioma Stem Cells.

Mostovenko E, Vegvari A, Rezeli M, Lichti C, Fenyo D, Wang Q ACS Chem Neurosci. 2017; 9(1):73-79.

PMID: 29254333 PMC: 6008157. DOI: 10.1021/acschemneuro.7b00362.

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